Wednesday, November 30, 2011

My brothers dream come true: baseball meets bioinformatics

James Fraser & Michael Eisen: Baseball Meets Biology


Letter of support for #UCDavis Chancellor cosigned by ~ 250 faculty #OccupyUCDavis

There was a letter published in the Davis Enterprise (Letter to the Editor – The Davis Enterprise) co-signed by many UC Davis Faculty. I have been sent the letter by Walter Leal, one of the coordinators of the distribution and signing, and he also sent the latest list of faculty signers (which has expanded greatly since the Enterprise letter was published). I am posting the letter and the latest list here. Note - I am also (slowly) adding links to web pages for the faculty so that people can find out more about who they are.

We, the undersigned UC Davis faculty, support the free exchange of ideas on campus and students’ right to peaceful protests. We are appalled by the events of Friday, Nov. 18 in the Quad, but heartened by the Chancellor's apology and her commitment to listen to and work on the students’ concerns. We strongly believe that Linda Katehi is well-qualified to lead our university through this difficult healing process and oppose the premature calls for her resignation; this is not in the best interest of our university.
  1. Walter S. Leal, Professor, Entomology
  2. Nina Amenta, Professor, Computer Science
  3. Francisco J. Samaniego, Distinguished Professor, Statistics
  4. Ricardo H. R. Castro, Assistant Professor, Chemical Engineering & Material Science
  5. Kevin Johnson, Professor and Dean, Law School (signing in his individual capacity)
  6. Eduardo Blumwald, Professor, Plant Sciences
  7. Miguel A. Mendez, Professor, Law School
  8. Maureen Stanton, Professor, Evolution and Ecology
  9. Miguel A. Marino, Distinguished Professor Emeritus, Hydrologic Sciences, Civil & Environmental Engineering, and Biological & Agricultural Engineering

Journal club today on bacteria in toilets - posting some notes here

I am heading a journal club discussion today of the following paper: PLoS ONE: Microbial Biogeography of Public Restroom Surfaces

I am going to use this page/post to put up some notes for the discussion.  Fortunately I have a good guide in this - Rob Dunn wrote a nice commentary/review for Scientific American blogs: Public bathrooms house thousands of kinds of bacteria

Stay tuned/come back to this page as I will be posting some more notes. Any suggestions for other things to look at/discuss would be welcome.

Notes (I note - I am copying much of the text from the paper not rewriting it.)

Tuesday, November 29, 2011

Town Hall #2 - Chancellor Katehi meets w/ Faculty/Staff; Katehi receives much support

Quick post regarding the Town Hall meeting at UC Davis between the administration and faculty and staff.  I am going to tell it through pictures and twitter posts (mostly mine, with a few responses).  Will really try to write up a more essayish post ASAP.  I tried to match pictures to comments but some may be mismatched - please forgive me.  

If you want the punch line - it is pretty simple - lots and lots of support for Chancellor Katehi from faculty at staff with a few dissenting points of view.  Very few argued for the need for resignation (I think Nathan Brown was the only one but I may be wrong - Josh Clover and possibly others may have also said something along these lines).  And most said something positive about Katehi although most of the positive things were about how good a Chancellor people think she has been not about her handling of this incident and its aftermath.  Anyway - here are some pics and tweets ... Also note I tried to record a few videos here and there and for some reason the only two that came out well were of two of the biggest critics of Katehi - Clover and Brown.  I am including those vids though if you only look at the vids you will get a mistaken impression regarding the amount of criticism vs. support for Katehi. 

Once again - banners are not allowed.  WTF?
The Tree of Life: Faculty and staff arriving for Town Hall meeting with Chamcellor
11/29/11 4:09 PM

@phylogenomics Why is the sign partially covered?
11/29/11 4:34 PM

Faculty and staff arriving for Town Hall meeting with Chamcellor

Faculty and staff arriving for Town Hall meeting with Chamcellor


Wondering - can UC really force me to sign new patent agreement?

Just got this email
Dear UC Colleague, When you first joined the University of California, you signed a Patent Acknowledgment or Agreement (depending on when you joined UC) as a condition of employment or your ability to use UC research resources and facilities. Because of recent court decisions in the case Stanford v. Roche, it is necessary for you to sign an amendment to that document.

This amendment clarifies the original intent of the Patent Acknowledgment or Agreement you signed: to assign to the University rights to inventions and patents you may conceive or develop while employed by UC, using UC research facilities and/or resources, or using gift, grant or contract funds received through the University.

What's Hot in Biology 2011? Why, the Genomic Encyclopedia paper I am senior author on #Yay?

And now back to some science. Got an email a few days ago from Nikos Kyrpides pointing to this: What's Hot in Biology - 2011. Very cool - the paper on the "Genomic Encyclopedia of Bacteria and Archaea" project that I coordinated (and for which I am the senior author) has been identified as the hot biology paper of November/December 2011 by "Science Watch". Plus they have a reasonably detailed story about it "BRANCHING OUT WITH PHYLOGENETICALLY DRIVEN GENOME SEQUENCING" by Jeremy Cherfas. I note - the project was done at the DOE-Joint genome Institute and involved an enormous number of people there (I have an Adjunct Appointment there). It was done in collaboration with the DSMZ - a microbial culture collection in Germany.

The paper A phylogeny driven genomic encyclopedia of bacteria and archaea apparently has been getting a lot of citations, which I guess is how it got picked as being "hot".

Monday, November 28, 2011

Letter to UC Davis Faculty from Academic Senate Chair Linda Bisson Regarding Pepper Spray Incident #OccupyUCDavis

Below is an email letter I just received from Linda Bisson the Chair of the UC Davis Academic Senate and I thought it might be of interest.  It contains many details regarding the pepper spray incident and response(s) that I have not seen described anywhere else.
Dear Colleagues:

Many of you have asked me to issue a preliminary assessment of the events occurring on November 18, 2011, and to describe the actions taken to date by me and Executive Council. I know I have asked extraordinary patience of you while I undertake the job that I was appointed to do as your Chair of the Davis Division of the Academic Senate. As a scientist it is not in my nature to get ahead of the data; as a faculty member I put the students first. When I saw the first video of the brutality on the quad I felt as if I had been stabbed in the heart, a feeling I know the majority of you share.

Just another Monday at #UCDavis: contentious UC regents meeting, a strike (sort of) & some occupying #OccupyUCDavis #OUCD

The Prelude

Well, today was interesting at UC Davis (and I note - it is only 5:15 PM as I start to write this).  Two major related events were happening on campus today.  First, there was a meeting of the UC Regents that had a presence on campus (more on this in a bit).  Second, partly in response to the Regents meeting, there was a call for a "Strike" by UC Davis students as well as "sympathy" events planned at all other UC Campuses (Cory Golden in the Davis Enterprise has a good summary of these two related events here).  I note, I am adding links to my posts about the various events for those interested.  I know this is a bit self centered but I think it may help explain my thinking on the various issues.

The momentum for the strike came from a rally on the UC Davis quad last Monday (see my post about that here: An exhausting and exhilarating day at the #OccupyUCDavis rally).  On that day there was enormous amount of passion to rise up and do something in response to the pepper spraying incident of last Friday (see my post about that day here: A day of almost pure joy in #DavisCA and at #UCDavis, until ... #OccupyUCDavis).  1000s of people were there and though the Chancellor of UC Davis Linda Katehi talked, she did not assuage the crowd much if at all.  Then there was a General Assembly of sorts, out in the quad, where a vote was taken to hold a "strike" on Monday the 28th (i.e., today).  Some of the passion clearly came from the pepper spraying incident itself, some of it came from ongoing frustration with financial issues (e.g., tuition hikes) and some of it came from dismay and/or disappointment at the UC Davis administrations role in the incident as well as their response (e.g., the Saturday Press Conference did not go so well: My accidental encounter with the #OccupyUCDavis crowd at #UCDavis #impressed).  And one thing that happened that day was the "re-occupation" of the UC Davis Quad - this time with more tents, a geodesic dome, and many people.

Crowd outside regents meeting #occupyucdavis

Crowd outside regents meeting #occupyucdavis


More signs showing up at #ucdavis portion of regents meeting #occupyucdavis

More signs showing up at #ucdavis portion of regents meeting #occupyucdavis


Brilliant someone brought a banner - against the rules but should have been allowed #occupyucdavis

Brilliant someone brought a banner - against the rules but should have been allowed #occupyucdavis


Ucdavis folks speaking at Regents meeting #occupyucdavis


Ucdavis folks speaking at Regents meeting #occupyucdavis


At the #ucdavis ARC where people are listening to regents meeting - only minor protests #occupyucdavis

At the #ucdavis ARC where people are listening to regents meeting - only minor protests #occupyucdavis


Some sort of bike accident at #ucdavis outside regents meeting

Some sort of bike accident at #ucdavis outside regents meeting


UC Davis News Release: "A Day of Civil Discourse & Peaceful Expression" - except when not allowed #Uggh #OccupyUCDavis

According to UC Davis news release (UC Davis News & Information :: Dateline :: UC Davis to host regents, "teach-ins")
"UC Davis is preparing for a day of civil discourse and peaceful expression, as the campus hosts members of the University of California Board of Regents and faculty and students organize “teach-ins” on public disinvestment in higher education, the Occupy movement and other topics." 
Yes, civil discourse and peaceful expression.  Should be an interesting day on campus.  More on this later from me.  But one thing about this news release really irks me.  It says 
"If you’re planning to attend the UC Davis portion of the audioconference, please be prepared for a search of backpacks – and don’t bring banners or bottled water, which will not be allowed in the ARC ballroom."
So let me get this straight.  A day of civil discourse and peaceful expression.  And also a day for the regents to discuss such issues.  But don't bring banners, because that would be bad why?

Saturday, November 26, 2011

UC Davis Academic Committee on Academic Freedom and Responsibility Statement re #OccupyUCDavis

Just got this email and it seems worth sharing

Dear Colleagues,

On Friday we sent all of you a link to the Faculty Code of Conduct that includes on page three a statement of academic freedom rights. The Davis Division of the Academic Senate Committee on Academic Freedom and Responsibility unanimously voted to issue the following statement:

"The UC Davis Academic Senate Committee on Academic Freedom and Responsibility (CAFR) condemns violence as well as directives and policies that are likely to lead to it.  The role of a university in society is to serve as a beacon of compassion and tolerance to foster thoughtful discourse. Academic freedom is the pilot light protecting knowledge production and should protect all members of the university engaged in civil discourse without fear or threat of coercive retaliation or physical harm.  In light of an emerging pattern of policies and behaviors counter to these principles, we call on all University of California administrators to undergo training in the importance of academic freedom and how to protect and foster it against financial, political, and social pressures. We also plan to review recent events in order to assess to what degree academic freedom rights were violated and to make policy recommendations to safeguard academic freedom at University of California campuses. - unanimously agreed by CAFR members"

Linda F. Bisson
Chair, Davis Division of the Academic Senate
Professor, Viticulture and Enology

Friday, November 25, 2011

Email from #OccupyUCDavis to #UCDavis faculty - Call for a General Strike

Just got this email about the call for a General Strike apparently from OccupyUCDavis folks. It was from someone I do not know named Eric Lee. Not sure if he is a UC Davis student or not.

Dear UC Davis Faculty Member,

On behalf of the 99.5% of students, faculty, and workers who voted in favor of a General Strike to be held this coming Monday, November 28th, we are asking that you cancel your scheduled classes or hold your class on the quad this coming Monday in solidarity with your fellow community members against the terrible acts of police brutality committed this past week on our campus.

Our call for a walk-out lies on a series of undeniable principles of equality and democracy that we all share:

1) The right to peacefully redress government for grievances of social inequality under the first amendment

2) The right to not be brutally beaten for exercising these rights

3) Teachers, TAs, professors, faculty, and staff have the right to tenure and a fair wage

4) Education is a social right and fee-increases and budget cuts are unnecessary given the obscene plundering of the economy by the richest Americans over the past years

5) The fight for education is synonymous with the fight for equality in all social realms: housing, food, healthcare, transportation, energy, etc.

6) The US Government’s prioritization of war and tax cuts for the rich above social services for working Americans is unjust and should be reversed

This is a call to join the walkout against police brutality and social inequality. We are making space and facilities (white boards, etc.) available for all who are interested in holding class on the quad. Any special requests by teachers and faculty will be accommodated to the best of our ability.

Please respond to this email letting us know which of the three options you will be choosing:

a) I plan to cancel all classes Monday

b) I plan to hold classes in the quad Monday

c) I do not plan to cancel classes and I do not support the fight for public education

Please let us know of your plans ASAP.

Thank you for your cooperation!

-Occupy UC Davis
- - -
Note: A link to the General Strike proposal can be found here:

Not sure how I feel about much of what is in this message (actually - messages since there is a lot of stuff in here). I note - I am not a fan of their request for responses where the only no option is "I do not plan to cancel classes and I do not support the fight for public education". Well, as I have said here, I am not sure how I feel about the plan for cancel classes but I strongly support public education. I note I am a big supporter of many parts of the OccupyUCDavis movement that I have seen. But the tone here suggests that if you are not with them on this, then you are against them. I don't like that style since I thought I was one of them in some ways. In addition, the vote that was held (if he is referring to the vote at the Assembly Monday) did not include faculty or workers as far as I know since I thought it was a student vote. At least, that is what people told me when I was there - I would have voted actually - but was told it was a student vote.

I note - as of 30 minutes ago I was planning on doing a teach in on Monday in the Quad and still hope to. But I confess I am a bit worried about the direction and tone of the OccupyUCDavis movement based on this email.

UPDATE - I presume this "Eric Lee" is the same as the one who wrote the following:
The “Pepper Spray Incident” and the Inevitable Radicalization of the UC Student Body

More science conference spam

Got this invitation a minute ago:

Dear Dr.Jonathan Eisen,

I am Monica Fu from the organizing committee of the 4thAnnual World Congress of Vaccine. Cordially, we invite you to give an oral presentation at Session 418: Japanese Encephalitis, Junin, Hendra and Nipah Vaccines about your recent work. In order that you can learn the conference details and scientific program quickly, I am pleased to send you a conference brochure in the attachment. You are appreciated to reply me with a speech title to my email:

Certainly, if you have any questions about the conference, please do not hesitate to contact me.

Sincerely yours,

Ms. Monica Fu
Organizing Committee of WCV-2012 

Only a minor complication.  Never worked on anything related to this.  Ahh - I love science conference spam.

Thursday, November 24, 2011

Hmm ... Tagxedo word cloud from my Tweets suggests I have been obsessed w/ #OccupyUCDavis recently

Playing around with Tagxedo - word cloud from my blog

ABC radio news story on Indoor Ecology

Quick post here and it is not about OccupyUCDavis
Check out the story from ABC news (Australia, that is): Indoor ecology - RN Future Tense - 24 November 2011. Their summary:
We're used to hearing about threats to our outdoor environment. But we rarely think about some of the challenges that we face in our indoor environment.
A growing number of researchers are interested in the idea of 'indoor ecology' - treating the indoors like the outdoors and studying the spaces that surround many of us every day.
It has a lot of good stuff about the Sloan Foundation program.

Wednesday, November 23, 2011

#UCDavis Chancellor Linda Katehi to have Town Hall w/ faculty and staff Tuesday #OccupyUCDavis

Just got this email:
Faculty and staff are invited to a town hall meeting on Tuesday, November 29, in Freeborn Hall from 4:00-5:30 p.m.  The meeting will be an open discussion with Chancellor Linda P.B. Katehi, Provost and Executive Vice Chancellor Ralph Hexter, and Matt Carmichael, Acting Chief of the UC Davis Police Department.

For background regarding the use of pepper spray against protesters last week and the campus response, please see Sincerely,
Linda P.B. Katehi

#UCDavis quad - a place for gatherings for a long time

I went by the UC Davis Quad (the scene of the pepper spray incident Friday) today after class and took a look at the growing camp.  I thought I would take some pics that I think symbolize the Quad in part to me.  The Quad is a place for relaxation much of the time.  And it is also a place for gatherings.  The fact that the current gathering has tents is perhaps unusual.  But the fact that students are gathering at the Quad to express themselves is not.  I hope people do not come away from the pepper spray story with a view that the Quad is somehow being taken over for "expression."  Whether you support the growing camp or not, the Quad is historically a place where expression comes in many forms.  Today, what stood out to me, were all the signs sitting there for student groups that are used for recruitment at various times.  Below is a slideshow of these signs:

And for those without flash I am inserting all the pics below ...

Not quite sure what this means re: UC Davis Academic Senate and proposed strike

Just got this email. Not sure what it means though ...

*This message is being sent on behalf of the Academic Senate*

The Divisional Chair and members of the Executive Council were invited to a meeting today with members of Occupy UC Davis. We were pleased to meet with these students who have been involved with a call for a general strike on Monday, November 28. The call can be found here. The general strike has been called in conjunction with a meeting of the Board of Regents to be held in part on the Davis campus on Monday. A link to the meeting call can be found here.

In making their decisions concerning their instructional activities on November 28, faculty should be aware of the contents of the Faculty Code of Conduct, which can be found here.

Should #UCDavis faculty "walkout" from teaching to "support" students? I do not think so

There has been a call for a general student strike on Monday at UC Davis.  This is partly in relation to the pepper spraying incident but apparently more about access to education and budget cuts and such.  I just got this message from the Dean of the College of Biological Sciences regarding this
To All Faculty, Students, and Staff:

Some of you may have heard or read that there will be a general strike on Monday, November 28, 2011.  Please note that the campus is open for business as usual and students should plan to attend courses as scheduled unless they hear otherwise directly from their instructor.  This expectation applies equally to all Faculty, Lecturers, Teaching Assistants, and Associates.

Please have a safe and restful holiday break.

James E.K. Hildreth, PhD, MD
College of Biological Sciences
University of California, Davis
Well, this could be a set up for some complex interactions Monday. As many who read this blog know, I am incredibly disturbed by the pepper spray incident.  I am also very upset about the budget cuts and the challenges facing students on campus.  I am committed to working to fix the things that are broken at UC Davis and to also help students in as many ways as possible deal with tuition and fee increases.

Reporting from #UCDavis Town Hall meeting re: #OccupyUCDavis

Well here is  quick post about the Town Hall meeting.  I went there at about 4:30 with one of the PhD students in my lab - Russell Neches.  We got to Freeborn and a line was forming outside.  Russell got in the line and I went to the front to make sure it was the right place to be.  I saw one of the students in my Intro Bio class and he said it was the right place to be.  So I then went inside to grab a drink and headed back to the line.  I then took a few pictures and and posted some comments on twitter.  I am intermixing my comments here with twitter posts and my pictures.  I note - I would use Storify for this but they make it hard to include pictures from picasa so I am going to have to do it this way.  I realized this post is a bit raw - but I am very tired and I need to try and get some other work done, so this is going to have to suffice for now.  I may try to enhance it with more text in a bit.

UPDATE: Video of the Town Hall Meeting is here.

Crowd starting to form outside Freeborn Hall for #occupyucdavis Town Hall - TV crews coming too
11/22/11 4:23 PM

AP Video report from #OccupyUCDavis Camp Tuesday AM

Tuesday AM at #OccupyUCDavis camp

Tuesday AM I went over to check out the OccupyUCDavis encampment that had been set up overnight.  It had grown quite a bit since I had left the night before.  I wandered around taking some pictures and also dropped off a case of homemade pluot jam to donate.  While I was there I witnessed a government meeting to discuss various rules and issues.  The first discussion was a concern about smoking.  The second discussion was a reminder / encouragement to behave appropriately (i.e., no violence, illegal acts, etc).  Seemed to be going pretty well. 

Lots of TV crews were wandering around again but not much else seemed to be happening. The geodesic dome was up.  I then headed off to work on the other side of campus (work - I remember what that was).  Pics are below.

Top 10 action items for Chancellor Katehi from David Jay Harris at Town Hall #OccupyUCDavis

Working on a blog post about yesterday but thought I would post this for now. David Jay Harris does a good job of suggesting things for Katehi to do moving forward.

Tuesday, November 22, 2011

Crowd has been let in to Freeborn Hall re #occupyucdavis

Crowd has been let in to Freeborn Hall re #occupyucdavis

Preview of one of the letters that may be read at Town Hall meeting re #occupyucdavis

Preview of one of the letters that may be read at Town Hall meeting re #occupyucdavis

Open Letter from #UCDavis Prof. Mau Stanton re: Chancellor Katehi and #OcuppyUCDavis

All - I am posting an open letter sent to a mailing list for the UC Davis Center for Population Biology from Prof. Maureen Stanton (with her permission). Mau is a Professor in the Evolution and Ecology Department and has just recently been appointed Vice Provost for Academic Affairs at UC Davis.
Dear CPB members:

I have been listening and reading with great interest to the ongoing discussion about Friday's pepper-spraying travesty, and the subsequent calls for Chancellor Katehi's resignation. I want to add just a few words about my own experiences with the Chancellor, and how they've shaped my desire that she use this awful experience to transform herself into a better leader, rather than resigning. (My thoughts are captured perfectly by my faculty colleague Nina Amenta, whose open letter to the Chancellor is available through the link in her email below.)

Excellent summary of #OccupyUCDavis rally from @aggietv via @bmcdb

Saw this here: AggieTV summary of yesterday’s General Assembly

And thought I would repost it since it is really useful.

I note - Aggie TV really is doing a phenomenal job with coverage.

And the BMCDB grad students blog and twitter posts are great too.

Town Hall at #UCDavis re #OccupyUCDavis 5-7PM Freeborn Hall

Given the current campus events, the Student Assistants to the Chancellor will host a Town Hall open to all students, faculty and staff. There will be an open campus dialogue and Q&A time. The Chancellor will make opening remarks.

Date: Tuesday, November 22
Time: 5:00-7:00pm
Location: Freeborn Hall

Thank you,

Respectfully yours,
Vice Chancellor's Office - Student Affairs
University of California, Davis
Davis, CA 95616

An exhausting and exhilarating day at the #OccupyUCDavis rally

A blur. That is what this day represents. A serious blur. I got up not so early, not so late, since my kids are off school this week. And I started prepping for my day about town. At 12 noon there was to be a rally of some kind in regard to the pepper spraying incident on campus.

I have been consumed with this issue since Friday when the spraying of protestors happened in the "quad" at UC Davis. And I had been posting relentlessly to twitter and my blog and posterous and Facebook and, well, all over. I had no idea how this day was going to play out. Would Chancellor Katehi show up to the rally? Would she speak? What would other people say? Would the tents go up again? How many people would show up? Would it be peaceful (I assumed yes). Would there be any police around? And so on.

After finally having breakfast, I was getting ready to leave when the REAL blurriness began:

Well that could be a bad omen for today
11/21/11 10:02 AM
A bad omen?  Uggh.  First I dug out my cycling glasses and put them on.  They are prescription but a bit weird looking.  And I was possibly going to have to wear them all day.  And then, of course, I posted a pic to twitter.  The responses made me less fretful.

Monday, November 21, 2011

All my pics/vids from #OccupyUCDavis Rally - will clean up later

Here is a slideshow of all my pics from today's events at UC Davis. I have only cleaned up/cropped/labelled a few but thought some might want to see the whole collection before I pick the top hits ... I note - as of 7 PM PST there are still a few hundred left to upload ...


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